1GA7

CRYSTAL STRUCTURE OF THE ADP-RIBOSE PYROPHOSPHATASE IN COMPLEX WITH GD+3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.

Gabelli, S.B.Bianchet, M.A.Bessman, M.J.Amzel, L.M.

(2001) Nat.Struct.Mol.Biol. 8: 467-472

  • DOI: 10.1038/87647
  • Primary Citation of Related Structures:  1G0S, 1G9Q

  • PubMed Abstract: 
  • Regulation of cellular levels of ADP-ribose is important in preventing nonenzymatic ADP-ribosylation of proteins. The Escherichia coli ADP-ribose pyrophosphatase, a Nudix enzyme, catalyzes the hydrolysis of ADP-ribose to ribose-5-P and AMP, compounds ...

    Regulation of cellular levels of ADP-ribose is important in preventing nonenzymatic ADP-ribosylation of proteins. The Escherichia coli ADP-ribose pyrophosphatase, a Nudix enzyme, catalyzes the hydrolysis of ADP-ribose to ribose-5-P and AMP, compounds that can be recycled as part of nucleotide metabolism. The structures of the apo enzyme, the active enzyme and the complex with ADP-ribose were determined to 1.9 A, 2.7 A and 2.3 A, respectively. The structures reveal a symmetric homodimer with two equivalent catalytic sites, each formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition and catalytic activity. The structures also suggest a role for the residues conserved in each Nudix subfamily. The Nudix motif residues, folded as a loop-helix-loop tailored for pyrophosphate hydrolysis, compose the catalytic center; residues conferring substrate specificity occur in regions of the sequence removed from the Nudix motif. This segregation of catalytic and recognition roles provides versatility to the Nudix family.


    Related Citations: 
    • The Versatility of the Nudix Hydrolases as Revealed by the ADP-ribose Pyrophosphatase
      Gabelli, S.B.,Bianchet, M.A.,Bessman, M.J.,Amzel, L.M.
      (2000) Thesis --: 1


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION
A, B
209Escherichia coli (strain K12)Gene Names: nudF (aspP, yqiE, yzzG)
EC: 3.6.1.13
Find proteins for Q93K97 (Escherichia coli (strain K12))
Go to UniProtKB:  Q93K97
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD3
Query on GD3

Download SDF File 
Download CCD File 
A, B
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.930α = 90.00
b = 67.890β = 90.00
c = 98.070γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance